Generalities

All code associated to this page can be found here (https://github.com/svalbuenaa/UlcerativeColitisBulkRNAseq)

Raw counts matrix

Obtaining metadata information

Patient IDs

Area from which samples were obtained

Ascending
Descending
Large
Rectum
Sigmoid
Tranverse

Lognormalization of counts

Most variable genes

Mean vs CoV for all genes

Mean vs CoV for most variable genes

Principal component analysis (PCA)

PCA with all genes

Scree plot

PCA Scores

PCA with 500 most variable genes

PCA Scores

Differential expression analysis

GO enrichment up and down-regulated genes

Differential expression analysis with edgeR

Construct edgeR DGElist object

Filter low-expressed genes

Normalization

Estimate dispersion

Using classic mode.

GO enrichment up and down-regulated genes